Note the elliptical callus formation, the limb alignment, and the distance between the osteotomy and the pin sites.
Using the first (best) alignment retumed, the distance of the 5' end of the target sequence from the 3' end of the mRNA or EST in the nr database was calculated.
The distances in the kinome tree are based on all the columns in the alignment, while the distances in the specificity tree only consider the selected DoS columns in the alignment.
To control for sampling error, full-length alignments were randomized by permuting the alignment columns after which the domains were extracted using the same coordinates as in the original alignment, and the distances were calculated as indicated above.
For all the BESs from a species, we stored the alignment position(s) on the chicken genome assembly, the length of the alignment in nucleotides, the distance along the chicken alignment between both ends in the case of a PBH, and the E-values associated with alignments.
The region of the locus was extended from the anchored alignment to both ends by using other alignments of the same query sequence meeting the following criteria: (1) the direction of the alignment was identical to that of the anchored alignments; and (2) the distance between the alignment from the region of the locus (which is a possible intron) was less than 1 Mb.
It measures the similarity between every row (column) and then takes the maximum alignment error as the distance.
If no alignment is found, the distance is set to 1.
The intuition underlying Equation (8) is that if the alignment is good, the distance of a sequence residue pair shall match well with that of their aligned template residue pair.
For each pair of taxa in an alignment, we plotted their "pairwise similarity distance" (i.e. y-coordinates: number of sites displaying different states, normalized by the alignment length), versus the distance separating these two taxa along the tree branches (i.e. x-coordinates: the sum of branch lengths from the two taxa to their common ancestor).
